Research workbench

Crystal structure of mouse MTH1 with 8-oxo-dgtp

Analyse Crystal structure of mouse MTH1 with 8-oxo-dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MZE
Type: protein
Length: 614 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 7,8-dihydro-8-oxoguanine triphosphatase
EC: 3.6.1.55, 3.6.1.56
UniProt: P53368
Ligands: 8DG, CU
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56)	protein	153	18% helix, 46% strand	P53368
C, D	7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56)	protein	154	18% helix, 44% strand	P53368

Ligands and binding sites

8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
CU · Copper (II) ion · metal · 4 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C, B, D
GOL · Glycerol · additive · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.79	0.81	90	8DG
2	175	0.73	0.90	27	8DG
3	193	0.73	0.89	30	8DG
4	76	0.36	0.77	15	empty
5	57	0.36	0.79	12	empty

Interfaces

3 interfaces between chains.

A–C · 407 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 397 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 301 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5MZE · Crystal structure of mouse MTH1 with 8-oxo-dGTP · the same entry in another collection · chain D against D, TM-score 1.00
P53368 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (P53368) · a predicted model of the same protein · chain D against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P53368
Elsewhere: RCSB PDB 5MZE · PDBe 5MZE · UniProt P53368

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.